Timothy J. Triche

This paper identifies an EZH2-driven immune evasion phenotype in FUS::ERG AML that is reversible with tazemetostat, offering a potential targeted therapy for high-risk acute leukemia.

The paper uses cfMeDIP-seq to analyze cell-free placental DNA methylation in maternal plasma, identifying enriched regions associated with preterm birth and IUGR.

The paper analyzes bone marrow microenvironment changes in HMA-resistant MDS patients treated with guadecitabine and atezolizumab, finding that long-term survivors show reduced immunosuppressive monocytes and expanded effector lymphocytes.

This paper evaluates NV103, a CD99-targeted irinotecan nanoparticle, showing 20-fold greater antitumor effect than free irinotecan in Ewing sarcoma with no toxicity.

The paper presents a scalable Non-negative Matrix Factorization of the Human Cell Census to create interpretable transcriptional programs for biological reasoning.

This paper introduces a novel targeted nanoparticle platform for cancer therapy, showing significant tumor reduction and complete ablation in preclinical models.

BifurcatoR identifies clinically relevant subgroups by analyzing variance patterns in biological data, revealing hidden structures in AML and obesity.

bamSliceR enables rapid, cross-cohort variant analysis by extracting and analyzing aligned reads from GDC data, identifying clinically relevant variants in leukemia cohorts.

This paper develops a probabilistic model for cell type deconvolution using single-molecule DNA methylation haplotypes, showing improved accuracy in detecting rare cell types.

This paper introduces synthetic spike-in controls for cfMeDIP-seq to enable accurate and reproducible quantification of DNA methylation, reducing batch effects and technical biases.

STORM-seq improves single-cell RNA sequencing by enhancing detection of non-coding transcripts and transcript-level complexity, revealing new cell states in human fallopian tube epithelium.

An Rcpp implementation brings non-negative matrix factorization to singular-value-decomposition-like runtimes on sparse single-cell matrices, adding a scaling diagonal that keeps regularization penalties consistent across random initializations.

Compartmap infers higher-order chromatin structure from scRNA-seq and scATAC-seq data, matching specialized chromatin capture methods and identifying clinically relevant structural alterations in single cells.

This study identifies epigenetic differences between cutaneous and plexiform neurofibromas that drive distinct RAS/MKK/P38 signaling and clinical behavior.

The paper identifies a rapid increase in the SARS-CoV-2 M gene mutation I82T and its association with a new sub-B.1 clade, suggesting potential biological fitness and implications for surveillance.

The paper introduces CARD, a database for SARS-CoV-2 genomic surveillance, enabling rapid variant identification and phylogenetic analysis of viral isolates.